Cargando…

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by c...

Descripción completa

Detalles Bibliográficos
Autores principales:	Novák, Petr, Ávila Robledillo, Laura, Koblížková, Andrea, Vrbová, Iva, Neumann, Pavel, Macas, Jiří
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499541/ https://www.ncbi.nlm.nih.gov/pubmed/28402514 http://dx.doi.org/10.1093/nar/gkx257

Ejemplares similares

Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae
por: Ávila Robledillo, Laura, et al.
Publicado: (2020)

Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing
por: Ávila Robledillo, Laura, et al.
Publicado: (2018)

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats
por: Vondrak, Tihana, et al.
Publicado: (2019)

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes
por: Macas, Jiří, et al.
Publicado: (2023)

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
por: Skennerton, Connor T., et al.
Publicado: (2013)

Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads
por: Vondrak, Tihana, et al.
Publicado: (2021)

Centromeres Off the Hook: Massive Changes in Centromere Size and Structure Following Duplication of CenH3 Gene in Fabeae Species
por: Neumann, Pavel, et al.
Publicado: (2015)

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
por: Tang, Xubo, et al.
Publicado: (2023)

Pathoscope: Species identification and strain attribution with unassembled sequencing data
por: Francis, Owen E., et al.
Publicado: (2013)

An analysis of the feasibility of short read sequencing
por: Whiteford, Nava, et al.
Publicado: (2005)

Survey of extrachromosomal circular DNA derived from plant satellite repeats
por: Navrátilová, Alice, et al.
Publicado: (2008)

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia
por: Macas, Jiří, et al.
Publicado: (2011)

Correction: Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia
por: Macas, Jiří, et al.
Publicado: (2011)

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae
por: Novák, Petr, et al.
Publicado: (2014)

Inferring short tandem repeat variation from paired-end short reads
por: Cao, Minh Duc, et al.
Publicado: (2014)

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads
por: Gohr, André, et al.
Publicado: (2023)

Short pyrosequencing reads suffice for accurate microbial community analysis
por: Liu, Zongzhi, et al.
Publicado: (2007)

FragGeneScan: predicting genes in short and error-prone reads
por: Rho, Mina, et al.
Publicado: (2010)

A sensitive repeat identification framework based on short and long reads
por: Liao, Xingyu, et al.
Publicado: (2021)

Dysgu: efficient structural variant calling using short or long reads
por: Cleal, Kez, et al.
Publicado: (2022)

StrainXpress: strain aware metagenome assembly from short reads
por: Kang, Xiongbin, et al.
Publicado: (2022)

Rapid, robust plasmid verification by de novo assembly of short sequencing reads
por: Gallegos, Jenna E, et al.
Publicado: (2020)

A cross-sample statistical model for SNP detection in short-read sequencing data
por: Muralidharan, Omkar, et al.
Publicado: (2012)

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
por: Dohm, Juliane C., et al.
Publicado: (2008)

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
por: Namiki, Toshiaki, et al.
Publicado: (2012)

Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes
por: Shin, GiWon, et al.
Publicado: (2019)

A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
por: Peng, Gongxin, et al.
Publicado: (2016)

De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines
por: Silva, Bráulio S. M. L., et al.
Publicado: (2019)

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions
por: Amir, Amnon, et al.
Publicado: (2013)

Accurate profiling of full-length Fv in highly homologous antibody libraries using UMI tagged short reads
por: Levin, Itay, et al.
Publicado: (2023)

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae
por: Macas, Jiří, et al.
Publicado: (2015)

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores
por: Orellana, Luis H., et al.
Publicado: (2017)

Disruption of the standard kinetochore in holocentric Cuscuta species
por: Neumann, Pavel, et al.
Publicado: (2023)

Functional sequencing read annotation for high precision microbiome analysis
por: Zhu, Chengsheng, et al.
Publicado: (2018)

Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads
por: Liu, Jiemeng, et al.
Publicado: (2019)

Binning unassembled short reads based on k-mer abundance covariance using sparse coding
por: Kyrgyzov, Olexiy, et al.
Publicado: (2020)

Long-read amplicon denoising
por: Kumar, Venkatesh, et al.
Publicado: (2019)

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains
por: Neumann, Pavel, et al.
Publicado: (2012)

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
por: Novák, Petr, et al.
Publicado: (2010)

Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes
por: Li, Yufeng, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_78d19pssb1r7abfcsp4bq916ic